To say that $a and $b are in main:: you can use something like:

package main;
our($a,$b);

package RealPackage;
# ...
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However, I think you are doing something that is not a good idea. Since you seem to have perl >=5.6, I would reccommend using a function with a prototype of ($$) as your sort routine:

sub directories_first ($$) {
   my ($a,$b) = @_;
   # ...
}
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Otherwise, if your function is to work should you want to use it in a package besides main you're going to need to do something to use the correct package's variable, such as dynamically generating the function on export or using symbolic references.